So grab and flash the 239MB KRT16S Android 4.4 OTA right now, no matter what your rooting/bootloader situation is. Of course, if you've modified the system partition in such a way that the OTA won't apply cleanly anymore, you have to either revert those changes and try again or flash the factory image.

Prerequisites

In order to complete the steps below, you need to have the Android SDK installed. The SDK contains the latest version of adb and fastboot, which you will need for flashing. You will also need a MicroUSB cable to execute adb sideload, fastboot flash, and other commands. You don't need a USB cable if you're just planning to download the OTA zip directly to your device and flash it using a custom recovery.

You must be running Android 4.3 JWR66Y or Android 4.4 KRT16O for this OTA to work.

Install

Note: This method, just like the native OTA update procedure, does not wipe your data, and your bootloader does not need to be unlocked. You should be able to use either the stock recovery or a custom one.

adb sideload the zip you downloaded above by following my earlier guide here. If something fails, try to fix it by restoring the system files you've changed or use the factory image.

Here's what you should expect to see if you're using the fine TWRP recovery: